Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome sequence and mutations of the Glioma model inbred C57BL/6 mice strain Hong-Zhi Gao, Ming-Xi Wang, Wei-Peng Hu, Jun-Yan Chen, Xiang-Rong Chen & Ling Lin To cite this article: Hong-Zhi Gao, Ming-Xi Wang, Wei-Peng Hu, Jun-Yan Chen, Xiang-Rong Chen & Ling Lin (2014): Complete mitochondrial genome sequence and mutations of the Glioma model inbred C57BL/6 mice strain, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.971256
Published online: 16 Oct 2014.
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Date: 07 November 2015, At: 20:15
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971256
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence and mutations of the Glioma model inbred C57BL/6 mice strain Hong-Zhi Gao1, Ming-Xi Wang2, Wei-Peng Hu1, Jun-Yan Chen1, Xiang-Rong Chen1, and Ling Lin3 Department of Neurosurgery, the Second Affliated Hospital of Fujian Medical University, Fuzhou, P.R. China, 2Department of Biomedicine, Huaqiao University, Fuzhou, P.R. China, and 3Department of Immunology, the Second Affliated Hospital of Fujian Medical University, Fuzhou, P.R. China
Downloaded by [Deakin University Library] at 20:15 07 November 2015
1
Abstract
Keywords
In the present work we undertook the complete mitochondrial genome sequencing of an important glioma model inbred rat strain for the first time. The total length of the mitogenome was 16,308 bp. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The mutation events were also reported.
Genome, Glioma, mitochondrion
Animals have been used by humans for centuries to understand their own biology. In glioma research, animal models have allowed the study of glioma disease in the early stages, as well as the investigation of the mechanisms of the pathogenesis of glioma disease and the effects of drug intervention (Jeitany et al., 2014). Gliomas are the most common primary malignant brain tumors, which comprise approximately one-third of intrinsic neoplasms of the central nervous system in both adults and children. It is a type of aggressive tumor with a tendency to invade the surrounding brain tissue. The patients diagnosed with glioblastoma multiforme (GBM, a grade IV glioma) remain poor prognosis despite implementation of intensive therapeutic strategies and clinical efforts. To date, the diagnosis of glioma before clinical treatment is mainly by computer tomography and nuclear magnetic resonance imaging. However, they are expensive and difficult to spread (Shao et al., 2014; Wang et al., 2014). Inbred rat and mouse strains with variations in their mitochondrial genomic sequences serve as good substrates for construction of conplastic strains for examining genetic contributions. Several complex traits are controlled by genetic elements of the mitochondrial genome (Yue et al., 2014). Here, we reported complete mitochondrial genome sequence of a glioma inbred C57BL/6 mice model. Total DNA was
History Received 10 September 2014 Accepted 19 September 2014 Published online 16 October 2014
extracted from the brain tissue of a female individual that harboring a serious glioma. Polymerase chain reaction (PCR) was carried out using 22 pairs of primers to amplify the entire mitochondrial genome. Mitochondrial DNA information of this strain was described in the Table 1 and sequence from the current study were deposited in GenBank (Accession No. KJ939361). The mitochondrial genome was 16,308 bp long including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The total length of the proteincoding gene sequences was 11,437 bp. Most protein-coding genes initiated with ATG except for ND2, ND3 and ND5 which began with ATA. Eight protein-coding genes terminated with TAA whereas the ND2, ND3 and COX3 genes terminates with TAG and the CytB gene terminates with AGA. The incomplete stop codon (T– –) is used in ND4. A strong bias against G at the third codon position is observed in the protein-coding genes. The length of tRNA genes vary from 60 to 73 bp. Sequence data obtained from the current study were compared with the reference BN sequence (AC_000022.1). Eighty-nine variations in mtDNA were observed between these two strains. 35.5% of the variations were within gene-coding sequences, 18.7% were within non-coding RNA sequences, and 45.8% were synonymous variants.
Correspondence: Ling Lin, The Second Affliated Hospital of Fujian Medical University, Fuzhou 350000, P.R. China. E-mail: [email protected]
2
H.-Z. Gao et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Genes encoded by this mitochondrial genome. Position Gene
Downloaded by [Deakin University Library] at 20:15 07 November 2015
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CytB tRNAThr tRNAPro
Base composition (%)
From
To
Size (bp)
A
C
G
T
362 432 1388 1455 3025 3102 4058 4124 4198 4267 5309 5377 5447 5520 5552 5619 5688 7230 7306 7375 8065 8130 8291 8971 9755 9824 10,171 10,240 10,530 11,908 11,978 12,039 12,110 13,914 14,442 14,515 15,658 15,727
429 1386 1454 3024 3099 4058 4126 4195 4266 5310 5375 5445 5519 5550 5618 5686 7232 7298 7373 8058 8127 8330 8971 9774 9823 10,180 10,239 10,536 11,907 11,977 12,037 12,109 13,930 14,441 14,510 15,654 15,727 15,789
67 955 67 1570 75 957 69 72 69 1044 67 69 73 31 67 68 1545 69 68 684 63 201 681 804 69 357 69 297 1378 70 60 71 1821 528 69 1140 70 66
35.8 36.8 38.8 37.7 33.3 31.9 40.6 25.0 27.5 36.4 37.3 27.6 23.3 35.5 25.4 33.8 28.8 26.1 36.8 34.2 34.9 39.8 33.6 26.5 31.9 30.3 40.6 32.3 32.3 41.4 31.7 38.0 32.7 22.2 29.0 31.2 34.3 24.2
25.4 22.7 19.4 21.0 21.3 27.9 13.0 9.7 24.6 26.4 20.9 10.1 16.4 29.0 20.9 16.2 25.3 14.5 13.2 23.8 17.5 23.9 27.4 28.7 18.8 29.4 10.1 24.6 28.2 15.7 18.3 14.1 29.3 8.7 11.6 30.2 21.4 13.7
17.9 18.0 11.9 17.7 16.0 12.6 14.5 29.2 18.9 8.9 16.4 23.2 31.5 25.8 25.4 20.6 16.3 27.5 17.6 14.6 17.5 7.9 11.1 14.8 16.0 12.9 10.1 11.5 10.9 8.6 16.7 18.3 10.5 28.2 20.3 13.4 17.1 28.8
20.9 22.5 29.9 23.6 29.4 27.6 31.9 36.1 29.0 28.3 25.4 39.1 28.8 9.7 28.3 29.4 29.6 31.9 32.4 27.4 30.1 28.4 27.9 30.0 33.3 27.4 39.2 31.6 28.6 34.3 33.3 29.6 27.5 40.9 39.1 25.2 27.2 33.3
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Jeitany M, Pineda JR, Liu Q, Porreca RM, Hoffschir F, Desmaze C, Silvestre DC, et al. (2014). A preclinical mouse model of glioma with an alternative mechanism of telomere maintenance (ALT). Int J Cancer. doi: 10.1002/ijc.29171.
Start codon
Stop codon
ATG
TAA
ATA
TAG
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATA
TAG
ATG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Strand H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L
Shao N, Wang L, Xue L, Wang R, Lan Q. (2014). Plasma miR-454-3p as a potential prognostic indicator in human glioma. Neurol Sci. doi: 10.1007/s10072-014-1938-7. Wang L, Chen L, Wang Q, Wang L, Wang H, Shen Y, Li X, et al. (2014). Circulating endothelial progenitor cells are involved in VEGFR2-related endothelial differentiation in glioma. Oncol Rep. doi: 10.3892/or.2014.3467. Yue H, Liu S, Liu Y, Zhang X, Fan Z. (2014). Mitochondrial genome of the Sichuan field mouse (Apodemus latronum). Mitochondrial DNA. doi: 10.3109/19401736.2014.930835.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome sequence and mutations of the Glioma model inbred C57BL/6 mice strain Hong-Zhi Gao, Ming-Xi Wang, Wei-Peng Hu, Jun-Yan Chen, Xiang-Rong Chen & Ling Lin To cite this article: Hong-Zhi Gao, Ming-Xi Wang, Wei-Peng Hu, Jun-Yan Chen, Xiang-Rong Chen & Ling Lin (2014): Complete mitochondrial genome sequence and mutations of the Glioma model inbred C57BL/6 mice strain, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.971256
Published online: 16 Oct 2014.
Submit your article to this journal
Article views: 15
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Deakin University Library]
Date: 07 November 2015, At: 20:15
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971256
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence and mutations of the Glioma model inbred C57BL/6 mice strain Hong-Zhi Gao1, Ming-Xi Wang2, Wei-Peng Hu1, Jun-Yan Chen1, Xiang-Rong Chen1, and Ling Lin3 Department of Neurosurgery, the Second Affliated Hospital of Fujian Medical University, Fuzhou, P.R. China, 2Department of Biomedicine, Huaqiao University, Fuzhou, P.R. China, and 3Department of Immunology, the Second Affliated Hospital of Fujian Medical University, Fuzhou, P.R. China
Downloaded by [Deakin University Library] at 20:15 07 November 2015
1
Abstract
Keywords
In the present work we undertook the complete mitochondrial genome sequencing of an important glioma model inbred rat strain for the first time. The total length of the mitogenome was 16,308 bp. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The mutation events were also reported.
Genome, Glioma, mitochondrion
Animals have been used by humans for centuries to understand their own biology. In glioma research, animal models have allowed the study of glioma disease in the early stages, as well as the investigation of the mechanisms of the pathogenesis of glioma disease and the effects of drug intervention (Jeitany et al., 2014). Gliomas are the most common primary malignant brain tumors, which comprise approximately one-third of intrinsic neoplasms of the central nervous system in both adults and children. It is a type of aggressive tumor with a tendency to invade the surrounding brain tissue. The patients diagnosed with glioblastoma multiforme (GBM, a grade IV glioma) remain poor prognosis despite implementation of intensive therapeutic strategies and clinical efforts. To date, the diagnosis of glioma before clinical treatment is mainly by computer tomography and nuclear magnetic resonance imaging. However, they are expensive and difficult to spread (Shao et al., 2014; Wang et al., 2014). Inbred rat and mouse strains with variations in their mitochondrial genomic sequences serve as good substrates for construction of conplastic strains for examining genetic contributions. Several complex traits are controlled by genetic elements of the mitochondrial genome (Yue et al., 2014). Here, we reported complete mitochondrial genome sequence of a glioma inbred C57BL/6 mice model. Total DNA was
History Received 10 September 2014 Accepted 19 September 2014 Published online 16 October 2014
extracted from the brain tissue of a female individual that harboring a serious glioma. Polymerase chain reaction (PCR) was carried out using 22 pairs of primers to amplify the entire mitochondrial genome. Mitochondrial DNA information of this strain was described in the Table 1 and sequence from the current study were deposited in GenBank (Accession No. KJ939361). The mitochondrial genome was 16,308 bp long including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The total length of the proteincoding gene sequences was 11,437 bp. Most protein-coding genes initiated with ATG except for ND2, ND3 and ND5 which began with ATA. Eight protein-coding genes terminated with TAA whereas the ND2, ND3 and COX3 genes terminates with TAG and the CytB gene terminates with AGA. The incomplete stop codon (T– –) is used in ND4. A strong bias against G at the third codon position is observed in the protein-coding genes. The length of tRNA genes vary from 60 to 73 bp. Sequence data obtained from the current study were compared with the reference BN sequence (AC_000022.1). Eighty-nine variations in mtDNA were observed between these two strains. 35.5% of the variations were within gene-coding sequences, 18.7% were within non-coding RNA sequences, and 45.8% were synonymous variants.
Correspondence: Ling Lin, The Second Affliated Hospital of Fujian Medical University, Fuzhou 350000, P.R. China. E-mail: [email protected]
2
H.-Z. Gao et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Genes encoded by this mitochondrial genome. Position Gene
Downloaded by [Deakin University Library] at 20:15 07 November 2015
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CytB tRNAThr tRNAPro
Base composition (%)
From
To
Size (bp)
A
C
G
T
362 432 1388 1455 3025 3102 4058 4124 4198 4267 5309 5377 5447 5520 5552 5619 5688 7230 7306 7375 8065 8130 8291 8971 9755 9824 10,171 10,240 10,530 11,908 11,978 12,039 12,110 13,914 14,442 14,515 15,658 15,727
429 1386 1454 3024 3099 4058 4126 4195 4266 5310 5375 5445 5519 5550 5618 5686 7232 7298 7373 8058 8127 8330 8971 9774 9823 10,180 10,239 10,536 11,907 11,977 12,037 12,109 13,930 14,441 14,510 15,654 15,727 15,789
67 955 67 1570 75 957 69 72 69 1044 67 69 73 31 67 68 1545 69 68 684 63 201 681 804 69 357 69 297 1378 70 60 71 1821 528 69 1140 70 66
35.8 36.8 38.8 37.7 33.3 31.9 40.6 25.0 27.5 36.4 37.3 27.6 23.3 35.5 25.4 33.8 28.8 26.1 36.8 34.2 34.9 39.8 33.6 26.5 31.9 30.3 40.6 32.3 32.3 41.4 31.7 38.0 32.7 22.2 29.0 31.2 34.3 24.2
25.4 22.7 19.4 21.0 21.3 27.9 13.0 9.7 24.6 26.4 20.9 10.1 16.4 29.0 20.9 16.2 25.3 14.5 13.2 23.8 17.5 23.9 27.4 28.7 18.8 29.4 10.1 24.6 28.2 15.7 18.3 14.1 29.3 8.7 11.6 30.2 21.4 13.7
17.9 18.0 11.9 17.7 16.0 12.6 14.5 29.2 18.9 8.9 16.4 23.2 31.5 25.8 25.4 20.6 16.3 27.5 17.6 14.6 17.5 7.9 11.1 14.8 16.0 12.9 10.1 11.5 10.9 8.6 16.7 18.3 10.5 28.2 20.3 13.4 17.1 28.8
20.9 22.5 29.9 23.6 29.4 27.6 31.9 36.1 29.0 28.3 25.4 39.1 28.8 9.7 28.3 29.4 29.6 31.9 32.4 27.4 30.1 28.4 27.9 30.0 33.3 27.4 39.2 31.6 28.6 34.3 33.3 29.6 27.5 40.9 39.1 25.2 27.2 33.3
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Jeitany M, Pineda JR, Liu Q, Porreca RM, Hoffschir F, Desmaze C, Silvestre DC, et al. (2014). A preclinical mouse model of glioma with an alternative mechanism of telomere maintenance (ALT). Int J Cancer. doi: 10.1002/ijc.29171.
Start codon
Stop codon
ATG
TAA
ATA
TAG
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATA
TAG
ATG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Strand H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L
Shao N, Wang L, Xue L, Wang R, Lan Q. (2014). Plasma miR-454-3p as a potential prognostic indicator in human glioma. Neurol Sci. doi: 10.1007/s10072-014-1938-7. Wang L, Chen L, Wang Q, Wang L, Wang H, Shen Y, Li X, et al. (2014). Circulating endothelial progenitor cells are involved in VEGFR2-related endothelial differentiation in glioma. Oncol Rep. doi: 10.3892/or.2014.3467. Yue H, Liu S, Liu Y, Zhang X, Fan Z. (2014). Mitochondrial genome of the Sichuan field mouse (Apodemus latronum). Mitochondrial DNA. doi: 10.3109/19401736.2014.930835.
